Andreas Scherer
A5009582530- Cancer Genomics and Diagnostics
- Genomics and Rare Diseases
- Gene expression and cancer classification
- Renal cell carcinoma treatment
- Molecular Biology Techniques and Applications
- Renal and related cancers
- Bioinformatics and Genomic Networks
- Chronic Kidney Disease and Diabetes
- Genomics and Phylogenetic Studies
- Renal Diseases and Glomerulopathies
- Single-cell and spatial transcriptomics
- Renal Transplantation Outcomes and Treatments
- Ferroptosis and cancer prognosis
- Cancer-related molecular mechanisms research
- RNA modifications and cancer
- Cell Image Analysis Techniques
- Epigenetics and DNA Methylation
- Pancreatic and Hepatic Oncology Research
- MicroRNA in disease regulation
- Health, Environment, Cognitive Aging
- Phagocytosis and Immune Regulation
- Software Engineering Research
- Statistical Methods in Clinical Trials
- Software Engineering Techniques and Practices
- Meta-analysis and systematic reviews
Institute for Molecular Medicine Finland
2016-2024
University of Helsinki
2016-2024
Heinrich Heine University Düsseldorf
2024
Düsseldorf University Hospital
2024
Finland University
2018-2021
Center for Translational Molecular Medicine
2021
Double Helix (United States)
2018-2019
University of Turku
2017
Global Biological Standards Institute
2017
Kone (Finland)
2010-2014
Batch effects are the systematic non-biological differences between batches (groups) of samples in microarray experiments due to various causes such as sample preparation and hybridization protocols. Previous work focused mainly on development methods for effective batch removal. However, their impact cross-batch prediction performance, which is one most important goals microarray-based applications, has not been addressed. This paper uses a broad selection data sets from Microarray Quality...
Characterization and integration of the genome, epigenome, transcriptome, proteome metabolome different datasets is difficult owing to a lack ground truth. Here we develop characterize suites publicly available multi-omics reference materials matched DNA, RNA, protein metabolites derived from immortalized cell lines family quartet parents monozygotic twin daughters. These references provide built-in truth defined by relationships among members information flow DNA RNA protein. We demonstrate...
Abstract Background Oncopanel genomic testing, which identifies important somatic variants, is increasingly common in medical practice and especially clinical trials. Currently, there a paucity of reliable reference samples having suitably large number pre-identified variants for properly assessing oncopanel assay analytical quality performance. The FDA-led Sequencing Quality Control Phase 2 (SEQC2) consortium analyze ten diverse cancer cell lines individually their pool, termed Sample A, to...
Abstract Background Reproducible detection of inherited variants with whole genome sequencing (WGS) is vital for the implementation precision medicine and a complicated process in which each step affects variant call quality. Systematically assessing reproducibility WGS impact needed understanding improving quality from WGS. Results To dissect factors involved WGS, we sequence triplicates eight DNA samples representing two populations on three short-read platforms using library kits six labs...
Certified RNA reference materials are indispensable for assessing the reliability of sequencing to detect intrinsically small biological differences in clinical settings, such as molecular subtyping diseases. As part Quartet Project quality control and data integration multi-omics profiling, we established four derived from immortalized B-lymphoblastoid cell lines members a monozygotic twin family. Additionally, constructed ratio-based transcriptome-wide datasets between two samples,...
Genomic DNA reference materials are widely recognized as essential for ensuring data quality in omics research. However, relying solely on datasets to evaluate the accuracy of variant calling results is incomplete, they limited benchmark regions. Therefore, it important develop that enable assessment detection performance across entire genome.
Chronic allograft rejection (CR) is the major cause of failure long-term graft survival and so far irreversible. Early prognosis CR by molecular markers before overt histologic manifestation would be a valuable aid for optimization treatment regimens design clinical trials. Oligonucleotide microarray-based approaches have proven to useful diagnosis variety diseases were chosen unbiased identification prognostic biomarkers.Renal biopsies taken at month 6 posttransplantation (PT) from two...
Topical corticosteroids and calcineurin inhibitors are well-known treatments of atopic dermatitis (AD) but differ in their efficacy side effects. We recently showed that betamethasone valerate (BM) although clinically more efficient impaired skin barrier repair contrast to pimecrolimus AD.This study elucidates the mode action topical BM cream AD.Lesional AD samples after treatment with either or were subjected gene expression profile analysis.Betamethasone resulted a significant reduction...
Formalin-fixed, paraffin-embedded (FFPE) tissues are an underused resource for molecular analyses. This proof of concept study aimed to compare RNAseq results from FFPE biopsies with the corresponding RNAlater® (Qiagen, Germany) stored samples clear cell renal carcinoma (ccRCC) patients investigate feasibility in archival tissue. From each 16 undergoing partial or full nephrectomy, four core biopsies, such as two specimens ccRCC and adjacent normal tissue, were obtained a 16g needle. One one...
Abstract With the rapid advancement of sequencing technologies, next generation (NGS) analysis has been widely applied in cancer genomics research. More recently, NGS adopted clinical oncology to advance personalized medicine. Clinical applications precision require accurate tests that can distinguish tumor-specific mutations from artifacts introduced during processes or data analysis. Therefore, there is an urgent need develop best practices mutation detection using and for standard...
Cytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types cancer other diseases. However, the wide variety approaches available to interrogate these has created need for harmonized materials, methods, rigorous benchmarking improve genome-wide methylome sequencing applications clinical basic research. Here, we present multi-platform assessment cross-validated...
Chronic renal allograft injury is often reflected by interstitial fibrosis (IF) and tubular atrophy (TA) without evidence of specific etiology. In most instances, IF/TA remains an irreversible disorder, representing a major cause long-term loss. As members the protease family metzincins functionally related genes are involved in fibrotic sclerotic processes extracellular matrix (ECM), we hypothesized their deregulation IF/TA. Gene expression protein level analyses using biopsies with...
Clear cell renal carcinoma (ccRCC) represents the most common type of kidney cancer with high mortality in its advanced stages. Our study aim was to explore correlation between tumor epithelial-to-mesenchymal transition (EMT) and patient survival. Renal biopsies tumorous adjacent nontumorous tissue were taken a 16 g needle from our patients (n = 26) undergoing partial or radical nephrectomy due ccRCC RNA sequencing libraries generated using Illumina TruSeq® Access library preparation...
Abstract: It has been suggested that the increased rate of bacterial infection in atopic dermatitis (AD) may be caused by reduced antimicrobial protein (AMP) expression. We were interested whether common treatments AD affect defense. investigated effects topically applied corticosteroids betamethasone valerate (BV) and triamacinolone acetonide (TA) those calcineurin inhibitor pimecrolimus for 3 weeks on AMP expression AD. BV TA treatment led to a significant reduction expression; human...